[R-sig-Debian] Multiple LibPaths in Fresh Install

[Patrick Richardson]

Dirk,

As I suspected. . . its done for a good reason. Thank you for the info.

Patrick

On Fri, 2011-03-04 at 18:54 -0600, Dirk Eddelbuettel wrote:
> On 4 March 2011 at 19:18, Patrick Richardson wrote:
> | Using: natty alpha-2
> | 
> | Could anyone englighten me (or point me to a self-enlightment page) as
> | to why when installing R using:
> | 
> | > apt-get install revolution-mkl r-revolution-revobase revolution-r r-base-core
> | 
> | There are 4 library paths available (installed by default):
> | 
> | > .libPaths()
> | [1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"      
> | [3] "/usr/lib/R/library"            "/usr/lib64/R/library" 
> | 
> | I'm wondering why; 1) 4 different librarys are created (i am sure there
> | is a good reason, I just don't know what it is).
> | 
> | 2) Can I consolidate all packages into one library? (my instinct says
> | no, and that trying it would break something)
> | 
> | Any advice (or direction to a "figure it out for yourself" page) would
> | be appreciated.
> 
> It's scheme once suggested to me by Fritz Leisch and Kurt Hornik of R Core
> which has served us all well for eight years. See /etc/R/Renviron for these
> comments:
> 
> -----------------------------------------------------------------------------
> R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-pc-linux-gnu-library/2.12'}
> #R_LIBS_USER=${R_LIBS_USER-'~/Library/R/2.12/library'}
> 
> # edd Apr 2003  Allow local install in /usr/local, also add a directory for
> #               Debian packaged CRAN packages, and finally the default dir 
> # edd Jul 2007  Now use R_LIBS_SITE, not R_LIBS
> R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'}
> -----------------------------------------------------------------------------
> 
> Now, some reasons why the scheme is good:
> 
> a) /usr/  !=  /usr/local, and by putting /usr/local first it becomes the
> default for R install.packages() etc meaning that R and dpkg / apt-get don't
> fight over files (as dpkg et al only use /usr and never, evrt
> /usr/local). Very important. Also means local installs get priority which is
> robust.
> 
> b) It splits /usr/lib/R/site-library off for r-cran-* packages for Debian.
> 
> c) It creates /usr/lib/R/library for core R packages. Fritz and Kurt
> suggested that.
> 
> d) In your list, [3] and [4] are the same thing, there is simply a lib64
> symlink so it is really just three.
> 
> And as I said, this worked well for thousands of user over an eight year
> period.  Suggestions for improvements are of course always welcome.
> 
> Hope this helps, Dirk
> 
> 
> | 
> | Best,
> | 
> | Patrick
> | 
> | > sessionInfo()
> | R version 2.12.1 (2010-12-16)
> | Platform: x86_64-pc-linux-gnu (64-bit)
> | 
> | locale:
> |  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
> |  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
> |  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8   
> |  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
> |  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
> | [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
> | 
> | attached base packages:
> | [1] stats     graphics  grDevices utils     datasets  methods   base
> | 
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